To be more specific ... Most computers (desktop anyways) have at least Two IDE controllers ... channel one and channel two. On each channel you have space for two devices ... typically labeled Device 0 and Device 1. Device 0 will be the device connected at the end of the cable (at least that is the way I look at it) If you use two devices on one cable, you must set the jumpers on the devices accordingly. Also use proper cables (80 conductor cables will do fine on any IDE device) The device on the end of the cable will be set for MASTER and the device in the middle of the cable will be set as SLAVE. In your case ... I would put drive 1 on the end of the cable for channel 1, and set it for MASTER. The CD burner will hook up at the middle of that same cable, and set it as SLAVE. Drive 2 .... will be on the end of the cable for channel 2 and set as MASTER, even if it's the only device connected to that cable. Later on down the road, you may decide to stick a DVD ROM or even just a plain old CD ROM drive in as SLAVE on the secondary channel. (saving wear and tear on the burner when doing plain reading)
Seeing as how the main purpose of a DAW is for recording to the harddrives and burning CD's last ... separate them drives. who cares about the speed of the CD burner. You should be burning your songs at a slow speed anyway to avoid errors. In essence ... you are using the harddrives more than you will be using the CD burner, so give um some elbow room ... split them dudes up. They will repay you with less headaches of having to hunt down the cause of pops and clicks and drop-outs.
-Ken
-Edit- If you bust open your case and find that there is not two connection points on your cables .... Fear not ... just go buy some new 80 conductor cables. You can even get some of them slick lookin round ones for fairly cheap now-a-days.